Ground Truth Curation
We integrated DrugMechDB with PrimeKG through a structured entity-mapping pipeline to create a benchmark-ready set of mechanistic pathways.
Data Pipeline
Source
DrugMechDB
5,666
Pathways
4,583
Indications
1,580
Drugs
744
Diseases
343 Pathways Mapped
→
Entity Mapping
Target
PrimeKG
129K+
Nodes
8.1M+
Edges
10
Entity Types
11
Relations
↓
Filter: pathways with 4+ nodes
Final Benchmark Set
150
Pathways
4–11 nodes
Quality Score
How much of the predicted pathway matches the mappable ground-truth mechanism.
Coverage Score
How much of the full original mechanism is recoverable inside PrimeKG.
Why it matters
These scores separate algorithmic failure from graph incompleteness and ontology mismatch.